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Scrimer: designing primers from transcriptome data
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SYSNO ASEP 0443615 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Scrimer: designing primers from transcriptome data Tvůrce(i) Mořkovský, Libor (UBO-W)
Pačes, Jan (UMG-J) RID, ORCID
Rídl, Jakub (UMG-J) ORCID
Reifová, R. (CZ)Celkový počet autorů 4 Zdroj.dok. Molecular Ecology Resources - ISSN 1755-098X
Roč. 15, č. 6 (2015), s. 1415-1420Poč.str. 6 s. Jazyk dok. eng - angličtina Země vyd. GB - Velká Británie Klíč. slova next-generation sequencing ; primer design ; SNaPshot ; SNP genotyping ; transcriptome Vědní obor RIV EB - Genetika a molekulární biologie CEP EE2.3.20.0303 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy Institucionální podpora UBO-W - RVO:68081766 ; UMG-J - RVO:68378050 UT WOS 000362838300015 EID SCOPUS 84943553772 DOI 10.1111/1755-0998.12403 Anotace With the rise of next-generation sequencing methods, it has become increasingly possible to obtain genomewide sequence data even for nonmodel species. Such data are often used for the development of single nucleotide polymorphism (SNP) markers, which can subsequently be screened in a larger population sample using a variety of genotyping techniques. Many of these techniques require appropriate locus-specific PCR and genotyping primers. Currently, there is no publicly available software for the automated design of suitable PCR and genotyping primers from next-generation sequence data. Here we present a pipeline called Scrimer that automates multiple steps, including adaptor removal, read mapping, selection of SNPs and multiple primer design from transcriptome data. The designed primers can be used in conjunction with several widely used genotyping methods such as SNaPshot or MALDI-TOF genotyping. Scrimer is composed of several reusable modules and an interactive bash workflow that connects these modules. Even the basic steps are presented, so the workflow can be executed in a step-by-step manner. The use of standard formats throughout the pipeline allows data from various sources to be plugged in, as well as easy inspection of intermediate results with visualization tools of the user’s choice. Pracoviště Ústav biologie obratlovců Kontakt Hana Slabáková, slabakova@ivb.cz, Tel.: 543 422 524 Rok sběru 2016
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